Copy number variations can be performed by hybridizing a labeled sample to an oligonucleotide array (see, e.g., Barrett et al. PNAS 2004 51:17765-70, Kidd et al. Nature 2008 453:56-64, U.S. Pat. No. 8,232,055) or by Fluorescent in situ Hybridization (FISH; e.g. Yamada et al, Cytogenet. Genome Res. 2011 132:248-54). However, such methods can sometimes prove challenging, particularly for low abundance samples. Low abundance samples can be amplified, e.g., using whole genome amplification (WGA) methods, prior to analysis. However, it is known that some sequences amplify more efficiently than others and, as such, use of such amplification methods can result in a bias towards some sequences, which increases signal noise. A solution to this problem is described herein.